In a report, it said "cynical deals" with Libya consigned thousands to the risk of drowning, rape and torture.
It said the EU was turning a blind eye to abuses in Libyan detention centres, and was mostly leaving it up to sea rescue charities to save migrants.
More than 2000 people have died in 2017 trying to get to Europe, it said.
The EU has so far made no public comments on Amnesty's report.
It comes as interior ministers from the 28-member bloc are meeting in Tallinn, Estonia, to discuss the migrant crisis.